A ligation DNAzyme-induced magnetic nanoparticles assembly for ultrasensitive detection of copper ions

Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme

DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.

DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging

DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.

Personal Glucose Meters Coupled with Signal Amplification Technologies for Quantitative Detection of Non-Glucose Targets: Recent Progress and Challenges in Food Safety Hazards Analysis

Ensuring food safety is paramount worldwide. Developing effective detection methods to ensure food safety can be challenging owing to trace hazards, long detection time, and resource-poor sites, in addition to the matrix effects of food. Personal glucose meter (PGM), a classic point-of-care testing device, possesses unique application advantages, demonstrating promise in food safety. Currently, many studies have used PGM-based biosensors and signal amplification technologies to achieve sensitive and specific detection of food hazards. Signal amplification technologies have the potential to greatly improve the analytical performance and integration of PGMs with biosensors, which is crucial for solving the challenges associated with the use of PGMs for food safety analysis. This review introduces the basic detection principle of a PGM-based sensing strategy, which consists of three key factors: target recognition, signal transduction, and signal output. Representative studies of existing PGM-based sensing strategies combined with various signal amplification technologies (nanomaterial-loaded multienzyme labeling, nucleic acid reaction, DNAzyme catalysis, responsive nanomaterial encapsulation, and others) in the field of food safety detection are reviewed. Future perspectives and potential opportunities and challenges associated with PGMs in the field of food safety are discussed. Despite the need for complex sample preparation and the lack of standardization in the field, using PGMs in combination with signal amplification technology shows promise as a rapid and cost-effective method for food safety hazard analysis.

An intelligent, autocatalytic, DNAzyme biocircuit for amplified imaging of intracellular microRNAs

DNAzymes hold great promise as transducing agents for the analysis of intracellular biomarkers. However, their low intracellular delivery efficiency and limited signal amplification capability (including an additional supply of cofactors) hinder their application in low-abundance biomarker analysis. Herein, a general strategy to design an intelligent, autocatalytic, DNAzyme biocircuit is developed for amplified microRNA imaging in living cells. The DNAzyme biocircuit is constructed based on a nanodevice composed of catalytic hairpin assembly (CHA) and DNAzyme biocatalytic functional units, sustained by Au nanoparticles (AuNPs) and MnO₂ nanosheets (CD/AM nanodevices). Once the CD/AM nanodevices are endocytosed by cells, the MnO₂ nanosheets are reduced by intracellular glutathione (GSH), which not only releases the different units of the DNAzyme circuit, but also generates the cofactor Mn²⁺ for DNAzyme autocatalysis. The intracellular analytes could trigger the coordinated cross-activation of CHA and autocatalytic DNAzymes on AuNPs, enabling reliable and accurate detection of miRNAs in living cells. This intelligent autocatalytic multilayer DNAzyme biocircuit can effectively avoid signal leakage and obtain high amplification gain, expanding the application of programmable complex DNA nanocircuits in biosensing, nanomaterial assembly, and biomedicine.

Using a Dendritic Sensor as a Feasible Method for Detection of Copper in Water Samples

Due to the severe dangers of copper on human health, development of identification and measurement copper methods in aquatic environments as well as prevention transfer methods of these substances to water resources have received much attention. Among of this expansion, rapid, simple, safe, sensitive and economically viable detection methods are more considerable. In this paper, the sensor activity of the poly(amidoamine) dendrimer containing eight methoxy groups modified with naphthalimide fluorescent derivative is studied. The sensor potential of dendrimer-naphthalimide fluorescence was evaluated in various solvents with different polarities, and results indicated that the detection of cuprum cations (Cu²⁺) is possible at low concentration. Also, the fluorescence properties of dendrimer-naphthalimide system are measured in the presence of diverse metal cations. In light of above, from the obtaining results, it can be concluded that dendritic sensor can be used as a feasible method to detect of copper in water samples in low concentrations.

Efficient adsorption of heavy metals from wastewater on nanocomposite beads prepared by chitosan and paper sludge

Chitosan was commonly used with inorganic salt and organic compounds to prepare adsorption material for water treatment. Different materials were mixed for the preparation, leading to a high cost for water treatment. Sludge from papermaking has abundant fiber and inorganic salt, which can reduce the addition of raw materials in preparing the adsorption material and thus lower the cost. This work used recycled industrial paper sludge to prepare adsorption material to remove heavy metals from wastewater. The adsorption properties of the prepared sludge-chitosan material for Cu²⁺ and Cr³⁺ in wastewater were investigated. The impacts of adsorption time, pH, and initial concentrations of Cu²⁺ and Cr³⁺ on adsorption amount were studied and optimized. The saturated adsorption capacity of sludge-chitosan material for Cu²⁺ and Cr³⁺ can reach 114.6 and 110.3 mg/g. The adsorption kinetics satisfied the pseudo-second-order model, indicating two modes, physical diffusion, and chem-sorption, in the heavy metal adsorption by the sludge-chitosan materials. Physical distribution has little Effect on chemical adsorption. The materials can be applied to treating Cu²⁺ and Cr³⁺ containing wastewater with the proposed cheap and readily available sludge-chitosan material. The results confirmed that sludge-chitosan material possessed good regeneration performance and was an ideal adsorbent.

DNA-only bioassay for simultaneous detection of proteins and nucleic acids

Testing multiple biomarkers, as opposed to one, has become a preferred approach for diagnosing many heterogeneous diseases, such as cancer and infectious diseases. However, numerous technologies, including gold standard ELISA and PCR, can detect only one type of biomarker, either protein or nucleic acid (NA), respectively. In this work, we report for the first time simultaneous detection of proteins and NAs in the same solution, using solely functional NA (FNA) molecules. In particular, we combined the thrombin binding aptamer (TBA) and the 10-23 RNA-cleaving DNA enzyme (DNAzyme) in a single aptazyme molecule (Aptazyme_1.15-3'), followed by extensive optimization of buffer composition, sequences and component ratios, to establish a competitive bioassay. Subsequently, to establish a multiplex bioassay, we designed a new aptazyme (Aptazyme_2.20-5') by replacing the target recognition and substrate sequences within Aptazyme_1.15-3'. This designing process included an in silico study, revealing the impact of the target recognition sequence on the aptazyme secondary structure and its catalytic activity. After proving the functionality of the new aptazyme in a singleplex bioassay, we demonstrated the capability of the two aptazymes to simultaneously detect thrombin and NA target, or two NA targets in a multiplex bioassay. High specificity in target detection was achieved with the limits of detection in the low nanomolar range, comparable to the singleplex bioassays. The presented results deepen the barely explored features of FNA for diagnosing multiple targets of different origins, adding an extra functionality to their catalogue.

A DNAzyme-based label-free fluorescent probe for guanosine-5'-triphosphate detection

Guanosine-5'-triphosphate (GTP) plays a key role in many important biological processes of cells. It is not only a primer for DNA replication and one of the four essential nucleoside triphosphates for mRNA synthesis, but also an energy source for translation and other important cellular processes. It can be converted to adenine nucleoside triphosphate (ATP), and the intracellular GTP level is closely related to the specific pathological state, so it is crucial to establish a simple and accurate method for the detection of GTP. Deoxyribozymes have unique catalytic and structural properties. One of the deoxyribozymes which is named DK2 with self-phosphorylation ability can transfer a phosphate from GTP to the 5' end in the presence of manganese(ii), while lambda exonuclease (λexo) catalyzes the gradual hydrolysis of double-stranded DNA molecules phosphorylated at the 5'-end from 5' to 3', but cannot cleave the 5'-OH end. The fluorescent dye SYBR Green I (SG I) can bind to dsDNA and produce significant fluorescence, but it can only give out weak fluorescence when it is mixed with a single strand. Here, we present a novel unlabeled fluorescence assay for GTP based on the self-phosphorylation of deoxyribozyme DK2 and the specific hydrolysis of λexo. Owing to the advantages of simple operation, high sensitivity, good specificity, low cost and without fluorophore (quenching group) labeling, this method has great potential in biological applications.

Bifunctional antibody and copper-based metal-organic framework nanocomposites for colorimetric α-fetoprotein sensing

Cu²⁺ are found to greatly reduce the photoinduced oxidase activity of fluorescein and then inhibit the chromogenic reaction catalyzed by fluorescein. A simple colorimetric assay for Cu²⁺ is established. Based on this, bifunctional nanocomposites of α-fetoprotein (AFP) antibody (Ab) and copper-based metal-organic framework (Ab2@Cu-MOF) are synthesized by the simple self-assembly of AFP Ab2, Cu²⁺, and 4,4'-dipyridyl: the binding site of AFP Ab2 exposed on the surface of the nanocomposites can specifically recognize AFP antigen; Cu²⁺ in nanocomposites can inhibit the visible light-induced activity of fluorescein. The structure of Ab2@Cu-MOF disintegrate and Cu²⁺ is released in an acetate buffer solution. The higher the amount of AFP antigens, the more significant the inhibitory effect. Thus, the Ab2@Cu-MOF immunoassay for AFP determination is established using 3,3',5,5'-tetramethylbenzidine as chromogenic substrate with a detection limit of 35 pg.mL^-1. This simple, cheap, and sensitive method sheds substantial light on practical clinical diagnosis. Meanwhile, the mechanism of inhibition is revealed to facilitate the targeted selection of enzyme regulators. Graphical abstract Diagrammatic illustration of Cu²⁺ detection (part a) and Ab2@Cu-MOF immunoassay for sensing α-fetoprotein based on the synthesized Ab2@Cu-MOF nanocomposites (parts a and b).

A simple and rapid technique for the determination of copper based on air-assisted liquid-liquid microextraction and image colorimetric analysis

In this study, a new, cheap, simple and rapid method for the determination of copper in water and food samples using air-assisted liquid-liquid microextraction and digital image decomposition into the primary colors Red (R), Green (G) and Blue (B) is introduced. In the proposed method, sodium diethyl-dithiocarbamate (Na-DDTC) and carbon tetrachloride (CCl4) were used as the chelating agent and extraction solvent, respectively. The digital images of the extraction phase were obtained using an Android mobile phone and analyzed using a free app (Color Grab). Then the value of the B channel was taken as the analytical signal. The effects of different parameters influencing the extraction efficiency were investigated and optimized. Under the optimal conditions, the limit of detection (LOD) and quantitation (LOQ) were 1.5 and 5 μg L-1, respectively. The repeatability of the proposed method, expressed as the relative standard deviation (RSD), was 4.53% for intra-day (n = 8, C = 100 μg L-1) and 5.66% for inter-day (n = 5) precision. The proposed method was applied for the determination of trace amounts of copper in rice, lettuce and water samples with satisfactory results validated by the Graphite Furnace Atomic Absorption Spectrometry technique.

Acid-Switchable DNAzyme Nanodevice for Imaging Multiple Metal Ions in Living Cells

Metal-assisted deoxyribozyme catalysis (DNAzyme) has been a general platform for constructing highly sensitive and selective detection sensors of metal ions. However, the "always on" mode of the traditional DNAzyme sensors greatly limits their application in the visual analysis of endogenous metal ions in a complex physiological microenvironment. To overcome this obstacle, a smart acid-switchable DNAzyme nanodevice is designed to control the DNAzyme activity in living cells and achieve simultaneous visualization of metal ions (Zn²⁺ and Pb²⁺) in situ. This nanodevice is built on DNAzyme precursors (DPs) and acid-switchable DNA (SW-DNA), precisely responding to pH variations in the range of 4.5-7.0, and the state of the three-strand hybridization of DPs successfully renders the DNAzymes inactive before being transported into cells. Once the nanodevice is taken up into living cells, the SW-DNA will change the configuration from linear to triplex in the acidic intracellular compartments (lysosomes, pH ∼4.5 to 5.0) and then the strands hybridized with the SW-DNA are liberated and subsequently react with DPs to form the active DNAzyme, which can further realize multi-imaging of intracellular metal ions. Moreover, this strategy has broad prospects as a powerful platform for constructing various acid-switchable nanodevices for visual analysis of multiple biomolecules in living cells.

Hairy Fluorescent Nanospheres Based on Polyelectrolyte Brush for Highly Sensitive Determination of Cu(II)

Currently, it is an ongoing challenge to develop fluorescent nanosphere detectors that are uniform, non-toxic, stable and bearing a large number of functional groups on the surface for further applications in a variety of fields. Here, we have synthesized hairy nanospheres (HNs) with different particle sizes and a content range of carboxyl groups from 4 mmol/g to 9 mmol/g. Based on this, hairy fluorescent nanospheres (HFNs) were prepared by the traditional coupling method (TCM) or adsorption-induced coupling method (ACM). By comparison, it was found that high brightness HFNs are fabricated based on HNs with poly (acrylic acid) brushes on the surface via ACM. The fluorescence intensity of hairy fluorescent nanospheres could be controlled by tuning the content of 5-aminofluorescein (5-AF) or the carboxyl groups of HNs easily. The carboxyl content of the HFNs could be as high as 8 mmol/g for further applications. The obtained HFNs are used for the detection of heavy metal ions in environmental pollution. Among various other metal ions, the response to Cu (II) is more obvious. We demonstrated that HFNs can serve as a selective probe and for the separation and determination of Cu(II) ions with a linear range of 0-0.5 μM and a low detection limit of 64 nM.

Biocompatible Ag2S quantum dots for highly sensitive detection of copper ions

An Ag₂S QD fluorescent sensor for highly selective and sensitive Cu²⁺ detection was developed and the quenching mechanism was investigated.

Liquid Cladding Mediated Optical Fiber Sensors for Copper Ion Detection

We present a label-free optical fiber based sensor device to detect copper ions (Cu2+) in water. A multimode optical fiber, with its polymer cladding removed along a 1-cm length, is used for the optical sensor head, where the injected Cu2+ in the liquid phase acts as a liquid cladding for the optical mode. The various Cu2+ concentrations modulate the numerical aperture (NA) of the liquid cladding waveguide part. The degree of NA mismatch between the liquid cladding and solid cladding guided parts gives rise to an optical power transmittance change, forming the sensing principle. The presented liquid cladding fiber sensor exhibits a minimum resolvable refractive index of 2.48 × 10-6. For Cu2+ detection, we functionalize the sensor head surface (fiber core) using chitosan conjugated ethylenediaminetetraacetic acid (EDTA) which captures Cu2+ effectively due to the enhanced chelating effects. We obtain a limit of detection of Cu2+ of 1.62 nM (104 ppt), which is significantly lower than the tolerable level in drinking water (~30 µM), and achieve a dynamic range of 1 mM. The simple structure of the sensor head and the sensing system ensures the potential capability of being miniaturized. This may allow for in-situ, highly-sensitive, heavy metal sensors in a compact format.

Single-molecule porphyrin-metal ion interaction and sensing application

It remains a significant challenge to study the interactions between metal ions and porphyrin molecules at single ion level. Here, we constructed a nanopore-based sensing for label-free and real-time analysis of the interaction between Cu²⁺ and 5,10,15,20-tetrakis(4-sulfonatophenyl)-porphyrin (TPPS). The results demonstrate that emerging electronic signatures of the Cu²⁺-TPPS complex that is completely different form the original free TPPS were observed in the α-hemolysin (α-HL) nanopore. Based on the distinctive electronic signal patterns between TPPS and Cu²⁺-TPPS complex, the unique nanopore sensor can achieve a highly sensitive detection of Cu²⁺ in aqueous media. The frequency of signature events showed a linear response toward the concentration of Cu²⁺ in the range of 0.03 µM - 1.0 μM, with a detection limit of 16 nM (S/N = 3). The sensing system also exhibited high selectivity against other metal ions, and the feasibility of this approach for practical applications was demonstrated with the determination of Cu²⁺ in running water.

Highly selective and sensitive method for Cu2+ detection based on chiroptical activity of L-Cysteine mediated Au nanorod assemblies

Herein, we demonstrated a simple and efficient method to detect Cu²⁺ based on amplified optical activity in the chiral nanoassemblies of gold nanorods (Au NRs). L-Cysteine can induce side-by-side or end-to-end assembly of Au NRs with an evident plasmonic circular dichroism (PCD) response due to coupling between surface plasmon resonances (SPR) of Au NRs and the chiral signal of L-Cys. Because of the obvious stronger plasmonic circular dichrosim (CD) response of the side-by-side assembly compared with the end-to-end assemblies, SS assembled Au NRs was selected as a sensitive platform and used for Cu²⁺ detection. In the presence of Cu²⁺, Cu²⁺ can catalyze O₂ oxidation of cysteine to cystine. With an increase in Cu²⁺ concentration, the L-Cysteine-mediated assembly of Au NRs decreased because of decrease in the free cysteine thiol groups, and the PCD signal decreased. Taking advantage of this method, Cu²⁺ could be detected in the concentration range of 20pM-5nM. Under optimal conditions, the calculated detection limit was found to be 7pM.

Recent Advances on Magnetic Relaxation Switching Assay-Based Nanosensors

Magnetic relaxation switching assay (MRSw)-based nanosensors respond to the changes of transverse relaxation time (T₂) of water molecules resulted from the analyte-induced aggregation and disaggregation of magnetic nanoparticles (MNPs). This strategy has been widely applied to the detections of various substrates from heavy metal ions to organic pollutants, proteins, nucleic acids, bacteria and viruses, and specific cells. Compared with other nanosensors, MRSw-based nanosensors not only are free from the background interferences, signal bleaching, and quenching but also overcome light scattering from samples without pretreatments. Therefore, MRSw-based nanosensors have been developed as real-time and on-site detection platforms for environmental protection, food safety, and risk assessment. This review summarizes the latest developments of the principles, the applicable magnetic nanoparticles, and the exploited environmental and biological applications of MRSw-based nanosensors.

Optomagnetic detection of DNA triplex nanoswitches

Triplex DNA formation is studied using rapid low-cost and dose-dependent optomagnetic method with an assay time of max 10 min and limit of detection of 100 pM.

Facile synthesis of multi-responsive functional graphene quantum dots for sensing metal cations

Aminated and phosphorylated graphene quantum dots (PiNGQDs) have been synthesized and used as fluorescent probes for sensing metal cations.

Room-temperature phosphorescence by Mn-doped ZnS quantum dots hybrid with Fenton system for the selective detection of Fe2+

Fe²⁺ was selectively detected based on the phosphorescence quenching of MPA–Mn : ZnS QDs caused by hydroxyl radicals from the Fenton reaction.

Mn-doped CdS/ZnS/CdS QD-based fluorescent nanosensor for rapid, selective, and ultrasensitive detection of copper(ii) ion

Energy levels of Mn-doped QD-based nanosensor and the quenching mechanism of the nanosensor by Cu²⁺.